deltaCaptureC
This is the released version of deltaCaptureC; for the devel version, see deltaCaptureC.
This Package Discovers Meso-scale Chromatin Remodeling from 3C Data
Bioconductor version: Release (3.23)
This package discovers meso-scale chromatin remodelling from 3C data. 3C data is local in nature. It givens interaction counts between restriction enzyme digestion fragments and a preferred 'viewpoint' region. By binning this data and using permutation testing, this package can test whether there are statistically significant changes in the interaction counts between the data from two cell types or two treatments.
Author: Michael Shapiro [aut, cre]
Maintainer: Michael Shapiro <michael.shapiro at crick.ac.uk>
citation("deltaCaptureC")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("deltaCaptureC")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("deltaCaptureC")| Delta Capture-C | HTML | R Script |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | BiologicalQuestion, Software, StatisticalMethod |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.6) |
| Imports | IRanges, GenomicRanges, SummarizedExperiment, ggplot2, DESeq2, tictoc |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | deltaCaptureC_1.26.0.tar.gz |
| Windows Binary (x86_64) | deltaCaptureC_1.26.0.zip |
| macOS Binary (big-sur-x86_64) | deltaCaptureC_1.26.0.tgz |
| macOS Binary (sonoma-arm64) | deltaCaptureC_1.26.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/deltaCaptureC |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/deltaCaptureC |
| Bioc Package Browser | https://code.bioconductor.org/browse/deltaCaptureC/ |
| Package Short Url | https://bioconductor.org/packages/deltaCaptureC/ |
| Package Downloads Report | Download Stats |